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• DNA is packed together with histones and other proteins into chromatin.
• Chromatin is a highly dynamic material which carries a substantial amount of epigentic information.
• All cells in the organism carry the same genetic material, however each cell type expresses different genes.
Epigenetics
• Epigenetics - Heritable changes in gene expression that operate outside of changes in DNA itself
Chromatin remodeling
• Protein expression can be induced and repressed over many orders of magnitude. An important part of this regulation is exerted via chromatin remodeling by DNA methylation and numerous modifications mainly of the N-termini of histones - acetylation, methylation, phosphorylation and ubiquitilation. There might be up to about 150 different such modifications !!!!
To be recognized as a CpG island, a sequence must satisfythe following critera:
1. (G+C) content of 0.50 or greater2. an observed to expected CpG dinucleotide ratio of 0.60 or greater3. and both occurring within a sequence window of 200 bp or greater.
CpGs are vastly underrepresented genome-widecompared to what would be expected by chance (0.23 inthe human genome and 0.19 in the mouse genome,respectively) This is because deamination of cytosine givesrise to uracil, which is easily recognized as foreign withinthe DNA strand and replaced, whereas deamination ofmethylcytosine gives rise to thymine, which is less readilyrecognized as foreign and therefore prone to mutationand depletion in the genome.
CpG island definition based on sequence compositionidentifies these elements at the promoter sites ofapproximately half of the genes in the human genome,most of which are expressed in most or all tissues, hencetheir designation as ‘housekeeping’ genes.
Southern blot based methylation assay
Unmethylated site
Me
Methylated site
- +
HpaII Probe MeHpaII Probe
- +
Methylation is globally erased during gametogenesis and embryogenesis
Kafri, T. , Ariel, M., Brandeis, M., Shemer, R., Urven, L., McCarrey, J ., Cedar,H. & Razin, A. (1992) Genes Dev 6, 705-714.
DNA demethylation of early embryos 3h 6h
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M
P
M
P
M
P
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8h Aphidicolin First met.
22h 2 cells 45h 4 cellsMayer, W., Niveleau, A., Walter, J ., Fundele, R. & Haaf, T. (2000) Nature403, 501-2
Establishment of DNA methylation pattern
• The methylation pattern of the genome is established anew every generation. In that sense methylation is an epigentic phenomenon - it influences the genetic material but it is not inherited from one generation to another.
• All methylation (or at least almost all) is erased during early embryogenesis and reestablished
DNMT3
Roles of DNA methylation
• Transcriptional silencing
• Protecting the genome from transposition
• Genomic imprinting
• X inactivation
• Tissue specific gene expression
Role of histone acetylation
• Acetylated histones open up the chromatin and enable transcription. Histones are acetylated by HAT (histone acetylases) which are parts of many chromatin remodeling and transcription complexes.
Role of histone de-acetylation
• Deacetylated histones are tightly packed and less accessible to transcription factors.
• Histones are deacetylated by HDAC (histone de-acetylase) proteins.
Epigenetic chromatin regulation
A. Modification at the DNA level
1. cytosine methylation
B. Histone modification - the histone code
1. Histone acetylation
2. Histone methylation
3. Histone phosphorylation
4. Histone ubiquitilation
5. Different types of histones
Genomic imprintingSome genes are expressed only from the maternal genome and some only
from the paternal genome
It is estimated that about 80 genes are imprinted and they can be found on
several different chromosomes
For example - igf2, h19, igf2r and genes involved in the Angelman and Prader Willi
syndromes